Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile.

A metagenomic analysis was performed on a soil profile from a wet tundra site in northern Alaska. The goal was to link existing biogeochemical knowledge of the system with the organisms and genes responsible for the relevant metabolic pathways. We specifically investigated how the importance of iron...

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Autores principales:	David A Lipson, John Matthew Haggerty, Archana Srinivas, Theodore K Raab, Shashank Sathe, Elizabeth A Dinsdale
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/436c848cd173490684cbb35decd8df33
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spelling	oai:doaj.org-article:436c848cd173490684cbb35decd8df332021-11-18T07:43:36ZMetagenomic insights into anaerobic metabolism along an Arctic peat soil profile.1932-620310.1371/journal.pone.0064659https://doaj.org/article/436c848cd173490684cbb35decd8df332013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23741360/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203A metagenomic analysis was performed on a soil profile from a wet tundra site in northern Alaska. The goal was to link existing biogeochemical knowledge of the system with the organisms and genes responsible for the relevant metabolic pathways. We specifically investigated how the importance of iron (Fe) oxides and humic substances (HS) as terminal electron acceptors in this ecosystem is expressed genetically, and how respiratory and fermentative processes varied with soil depth into the active layer and into the upper permafrost. Overall, the metagenomes reflected a microbial community enriched in a diverse range of anaerobic pathways, with a preponderance of known Fe reducing species at all depths in the profile. The abundance of sequences associated with anaerobic metabolic processes generally increased with depth, while aerobic cytochrome c oxidases decreased. Methanogenesis genes and methanogen genomes followed the pattern of CH4 fluxes: they increased steeply with depth into the active layer, but declined somewhat over the transition zone between the lower active layer and the upper permafrost. The latter was relatively enriched in fermentative and anaerobic respiratory pathways. A survey of decaheme cytochromes (MtrA, MtrC and their homologs) revealed that this is a promising approach to identifying potential reducers of Fe(III) or HS, and indicated a possible role for Acidobacteria as Fe reducers in these soils. Methanogens appear to coexist in the same layers, though in lower abundance, with Fe reducing bacteria and other potential competitors, including acetogens. These observations provide a rich set of hypotheses for further targeted study.David A LipsonJohn Matthew HaggertyArchana SrinivasTheodore K RaabShashank SatheElizabeth A DinsdalePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 5, p e64659 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q David A Lipson John Matthew Haggerty Archana Srinivas Theodore K Raab Shashank Sathe Elizabeth A Dinsdale Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile.
description	A metagenomic analysis was performed on a soil profile from a wet tundra site in northern Alaska. The goal was to link existing biogeochemical knowledge of the system with the organisms and genes responsible for the relevant metabolic pathways. We specifically investigated how the importance of iron (Fe) oxides and humic substances (HS) as terminal electron acceptors in this ecosystem is expressed genetically, and how respiratory and fermentative processes varied with soil depth into the active layer and into the upper permafrost. Overall, the metagenomes reflected a microbial community enriched in a diverse range of anaerobic pathways, with a preponderance of known Fe reducing species at all depths in the profile. The abundance of sequences associated with anaerobic metabolic processes generally increased with depth, while aerobic cytochrome c oxidases decreased. Methanogenesis genes and methanogen genomes followed the pattern of CH4 fluxes: they increased steeply with depth into the active layer, but declined somewhat over the transition zone between the lower active layer and the upper permafrost. The latter was relatively enriched in fermentative and anaerobic respiratory pathways. A survey of decaheme cytochromes (MtrA, MtrC and their homologs) revealed that this is a promising approach to identifying potential reducers of Fe(III) or HS, and indicated a possible role for Acidobacteria as Fe reducers in these soils. Methanogens appear to coexist in the same layers, though in lower abundance, with Fe reducing bacteria and other potential competitors, including acetogens. These observations provide a rich set of hypotheses for further targeted study.
format	article
author	David A Lipson John Matthew Haggerty Archana Srinivas Theodore K Raab Shashank Sathe Elizabeth A Dinsdale
author_facet	David A Lipson John Matthew Haggerty Archana Srinivas Theodore K Raab Shashank Sathe Elizabeth A Dinsdale
author_sort	David A Lipson
title	Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile.
title_short	Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile.
title_full	Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile.
title_fullStr	Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile.
title_full_unstemmed	Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile.
title_sort	metagenomic insights into anaerobic metabolism along an arctic peat soil profile.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/436c848cd173490684cbb35decd8df33
work_keys_str_mv	AT davidalipson metagenomicinsightsintoanaerobicmetabolismalonganarcticpeatsoilprofile AT johnmatthewhaggerty metagenomicinsightsintoanaerobicmetabolismalonganarcticpeatsoilprofile AT archanasrinivas metagenomicinsightsintoanaerobicmetabolismalonganarcticpeatsoilprofile AT theodorekraab metagenomicinsightsintoanaerobicmetabolismalonganarcticpeatsoilprofile AT shashanksathe metagenomicinsightsintoanaerobicmetabolismalonganarcticpeatsoilprofile AT elizabethadinsdale metagenomicinsightsintoanaerobicmetabolismalonganarcticpeatsoilprofile
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Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile.

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